gam 0.1.16

# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
#
# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
# with all versions of Cargo and also rewrite `path` dependencies
# to registry (e.g., crates.io) dependencies.
#
# If you are reading this file be aware that the original Cargo.toml
# will likely look very different (and much more reasonable).
# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
rust-version = "1.93"
name = "gam"
version = "0.1.16"
build = "build.rs"
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
default-run = "gam"
description = "Generalized penalized likelihood engine"
readme = "README.md"
license = "AGPL-3.0-or-later"

[package.metadata.cargo-machete]
ignored = [
    "grep",
    "walkdir",
]

[lib]
name = "gam"
path = "src/lib.rs"

[[bin]]
name = "gam"
path = "src/main.rs"

[[example]]
name = "validate_task24"
path = "examples/validate_task24.rs"

[[test]]
name = "alo_tests"
path = "tests/alo_tests.rs"

[[test]]
name = "aniso_integration"
path = "tests/aniso_integration.rs"

[[test]]
name = "aniso_population_calibration"
path = "tests/aniso_population_calibration.rs"

[[test]]
name = "autodiff_binomial_location_scale_exact"
path = "tests/autodiff_binomial_location_scale_exact.rs"

[[test]]
name = "autodiff_crosscheck"
path = "tests/autodiff_crosscheck.rs"

[[test]]
name = "autodiff_crosscheck_extended"
path = "tests/autodiff_crosscheck_extended.rs"

[[test]]
name = "autodiff_custom_family_joint_laml"
path = "tests/autodiff_custom_family_joint_laml.rs"

[[test]]
name = "autodiff_custom_family_pseudo_laplace"
path = "tests/autodiff_custom_family_pseudo_laplace.rs"

[[test]]
name = "autodiff_gaussian_location_scale_exact"
path = "tests/autodiff_gaussian_location_scale_exact.rs"

[[test]]
name = "autodiff_sas_hypergradient_localization"
path = "tests/autodiff_sas_hypergradient_localization.rs"

[[test]]
name = "biobank_convergence_regression"
path = "tests/biobank_convergence_regression.rs"

[[test]]
name = "biobank_dense_regression_guard"
path = "tests/biobank_dense_regression_guard.rs"

[[test]]
name = "biobank_margslope_repro"
path = "tests/biobank_margslope_repro.rs"

[[test]]
name = "biobank_reml_stress"
path = "tests/biobank_reml_stress.rs"

[[test]]
name = "dual_risk_test"
path = "tests/dual_risk_test.rs"

[[test]]
name = "duchon_integration"
path = "tests/duchon_integration.rs"

[[test]]
name = "exact_oracle_tests"
path = "tests/exact_oracle_tests.rs"

[[test]]
name = "external_gradient_trend"
path = "tests/external_gradient_trend.rs"

[[test]]
name = "firth_behavior"
path = "tests/firth_behavior.rs"

[[test]]
name = "gradient_decompose_test"
path = "tests/gradient_decompose_test.rs"

[[test]]
name = "gradient_isolation"
path = "tests/gradient_isolation.rs"

[[test]]
name = "ground_truth_gradient"
path = "tests/ground_truth_gradient.rs"

[[test]]
name = "margslope_flex_biobank_repro"
path = "tests/margslope_flex_biobank_repro.rs"

[[test]]
name = "margslope_inner_pirls_scaling"
path = "tests/margslope_inner_pirls_scaling.rs"

[[test]]
name = "matern_integration"
path = "tests/matern_integration.rs"

[[test]]
name = "no_production_finite_differences"
path = "tests/no_production_finite_differences.rs"

[[test]]
name = "power_law_analyzer"
path = "tests/power_law_analyzer.rs"

[[test]]
name = "probit_integration"
path = "tests/probit_integration.rs"

[[test]]
name = "repro_gamlss_linesearch_failure"
path = "tests/repro_gamlss_linesearch_failure.rs"

[[test]]
name = "sas_mixture_system"
path = "tests/sas_mixture_system.rs"

[[test]]
name = "standard_gam_scaling"
path = "tests/standard_gam_scaling.rs"

[[test]]
name = "stateful_saved_model_sync"
path = "tests/stateful_saved_model_sync.rs"

[[test]]
name = "subsample_outer_integration"
path = "tests/subsample_outer_integration.rs"

[[test]]
name = "survival_optimizer_api"
path = "tests/survival_optimizer_api.rs"

[[test]]
name = "survival_regression"
path = "tests/survival_regression.rs"

[[test]]
name = "thin_plate_integration"
path = "tests/thin_plate_integration.rs"

[[test]]
name = "tps_smallk_basis_regression"
path = "tests/tps_smallk_basis_regression.rs"

[[test]]
name = "uncertainty_integration"
path = "tests/uncertainty_integration.rs"

[[test]]
name = "warm_start_quality_regression"
path = "tests/warm_start_quality_regression.rs"

[[bench]]
name = "branch_cell_biobank_hv"
path = "benches/branch_cell_biobank_hv.rs"
harness = false

[[bench]]
name = "bvn_biobank_shape"
path = "benches/bvn_biobank_shape.rs"
harness = false

[[bench]]
name = "cell_moment_lru_biobank_shape"
path = "benches/cell_moment_lru_biobank_shape.rs"
harness = false

[[bench]]
name = "closed_form_criterion"
path = "benches/closed_form_criterion.rs"
harness = false

[[bench]]
name = "closed_form_pair_block"
path = "benches/closed_form_pair_block.rs"
harness = false

[[bench]]
name = "closed_form_perf"
path = "benches/closed_form_perf.rs"

[[bench]]
name = "margslope_flex_biobank_hv"
path = "benches/margslope_flex_biobank_hv.rs"
harness = false

[[bench]]
name = "non_affine_cell_hv_shape"
path = "benches/non_affine_cell_hv_shape.rs"
harness = false

[[bench]]
name = "spatial_basis_construction"
path = "benches/spatial_basis_construction.rs"
harness = false

[[bench]]
name = "trust_region_line_search"
path = "benches/trust_region_line_search.rs"
harness = false

[dependencies.approx]
version = "0.5.1"

[dependencies.arrow]
version = "54"
features = ["ffi"]
default-features = false

[dependencies.clap]
version = "4.6.0"
features = ["derive"]

[dependencies.comfy-table]
version = "7.2.2"

[dependencies.crossterm]
version = "0.29.0"

[dependencies.csv]
version = "1.4.0"

[dependencies.dyn-stack]
version = "0.13.2"

[dependencies.faer]
version = "0.24.0"

[dependencies.general-mcmc]
version = "0.9.0"
default-features = false
package = "general-mcmc"

[dependencies.indicatif]
version = "0.18.4"

[dependencies.log]
version = "0.4.29"

[dependencies.ndarray]
version = "0.17.2"
features = [
    "serde",
    "rayon",
]

[dependencies.opt]
version = "0.2.2"

[dependencies.parquet]
version = "54"
features = [
    "arrow",
    "snap",
    "zstd",
    "lz4",
]
default-features = false

[dependencies.pest]
version = "2.8.6"

[dependencies.pest_derive]
version = "2.8.6"

[dependencies.rand]
version = "0.10.0"

[dependencies.rand_distr]
version = "0.6.0"

[dependencies.ratatui]
version = "0.30.0"

[dependencies.rayon]
version = "1.11.0"

[dependencies.serde]
version = "1.0.228"
features = ["derive"]

[dependencies.serde_json]
version = "1.0.149"

[dependencies.smallvec]
version = "1"

[dependencies.statrs]
version = "0.18.0"

[dependencies.tempfile]
version = "3.27.0"

[dependencies.thiserror]
version = "2.0.18"

[dependencies.wide]
version = "0.7"

[dependencies.zip]
version = "8.2.0"
features = ["deflate"]
default-features = false

[dev-dependencies.ad_trait]
version = "0.2.2"

[dev-dependencies.autodiff]
version = "0.7.0"

[dev-dependencies.criterion]
version = "0.5"

[dev-dependencies.num-dual]
version = "0.13.6"

[lints.rust]
warnings = "deny"

[profile.release]
lto = "thin"
codegen-units = 1

[profile.release-dev]
lto = false
codegen-units = 16
debug = 0
inherits = "release"